/ - Diff - DockOnSurf - Forge du Centre Blaise Pascal

Révision b75bf97d

         return h_acceptor
     def get_use_molec_file():
         use_molec_file = dos_inp.get('Screening', 'use_molec_file',
                                      fallback='False')
         if use_molec_file in turn_false_answers:
             return False
         if not os.path.isfile(use_molec_file):
             logger.error(f'File {use_molec_file} not found.')
             raise FileNotFoundError(f'File {use_molec_file} not found')
         return use_molec_file
     # Refinement
     def get_refine_inp_file():  # TODO if not specified try isol_inp_file.
-...
             inp_vars['collision_threshold'] = get_coll_thrsld()
             inp_vars['min_coll_height'] = get_min_coll_height(
                 inp_vars['surf_norm_vect'])
             inp_vars['h_donor'] = get_H_donor(inp_vars['special_atoms'])
             inp_vars['max_structures'] = get_max_structures()
             if inp_vars['min_coll_height'] is False \
                     and inp_vars['collision_threshold'] is False:
                 logger.warning("Collisions are deactivated: Overlapping of "
                                "adsorbate and surface is possible")
             inp_vars['h_donor'] = get_H_donor(inp_vars['special_atoms'])
             inp_vars['max_structures'] = get_max_structures()
             inp_vars['use_molec_file'] = get_use_molec_file()
             # Options depending on the value of others
             if inp_vars['set_angles'] == "chemcat":

         logger.info('Carrying out procedures for the screening of adsorbate-surface'
                     ' structures.')
         if not os.path.isdir("isolated"):
             err = "'isolated' directory not found. It is needed in order to carry "
             "out the screening of structures to be adsorbed"
             logger.error(err)
             raise FileNotFoundError(err)
         if inp_vars['use_molec_file']:
             selected_confs = [adapt_format('ase', inp_vars['use_molec_file'])]
             logger.info(f"Using '{inp_vars['use_molec_file']}' as only conformer.")
         else:
             if not os.path.isdir("isolated"):
                 err = "'isolated' directory not found. It is needed in order to " \
                       "carry out the screening of structures to be adsorbed"
                 logger.error(err)
                 raise FileNotFoundError(err)
         finished_calcs, unfinished_calcs = check_finished_calcs('isolated',
                                                                 inp_vars['code'])
         if not finished_calcs:
             err_msg = "No calculations on 'isolated' finished normally."
             logger.error(err_msg)
             raise FileNotFoundError(err_msg)
         logger.info(f"Found {len(finished_calcs)} structures of isolated "
                     f"conformers whose calculation finished normally.")
         if len(unfinished_calcs) != 0:
             logger.warning(f"Found {len(unfinished_calcs)} calculations more that "
                            f"did not finish normally: {unfinished_calcs}. \n"
                            f"Using only the ones that finished normally: "
                            f"{finished_calcs}.")
         conformer_atoms_list = collect_coords(finished_calcs, inp_vars['code'],
                                               'isolated', inp_vars['special_atoms'])
         selected_confs = select_confs(conformer_atoms_list, finished_calcs,
                                       inp_vars['select_magns'],
                                       inp_vars['confs_per_magn'],
                                       inp_vars['code'])
             correct_calcs, failed_calcs = check_finished_calcs('isolated',
                                                                inp_vars['code'])
             if not correct_calcs:
                 err_msg = "No calculations on 'isolated' finished normally."
                 logger.error(err_msg)
                 raise FileNotFoundError(err_msg)
             logger.info(f"Found {len(correct_calcs)} structures of isolated "
                         f"conformers whose calculation finished normally.")
             if len(failed_calcs) != 0:
                 logger.warning(
                     f"Found {len(failed_calcs)} calculations more that "
                     f"did not finish normally: {failed_calcs}. \n"
                     f"Using only the ones that finished normally: "
                     f"{correct_calcs}.")
             conformer_atoms_list = collect_coords(correct_calcs, inp_vars['code'],
                                                   'isolated',
                                                   inp_vars['special_atoms'])
             selected_confs = select_confs(conformer_atoms_list, correct_calcs,
                                           inp_vars['select_magns'],
                                           inp_vars['confs_per_magn'],
                                           inp_vars['code'])
         surf = adapt_format('ase', inp_vars['surf_file'], inp_vars['special_atoms'])
         surf_ads_list = adsorb_confs(selected_confs, surf, inp_vars)
         if len(surf_ads_list) > inp_vars['max_structures']:

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Chimie Théorique » scripts_chimie4psmn » DockOnSurf

Révision b75bf97d